Biology subjects

Kilic, E.

Publications and source records attributed to Kilic, E..

17 recordsLinked to original sources

bioRxiv2026

Circadian multimodal physiological, ocular and behavioural data from a 40-hour forced-desynchrony protocol

We present a multimodal dataset from twelve healthy adults (aged 19-30 years, 50% female) who completed a 40-hour ultra-short sleep-wake forced desynchrony protocol which scheduled 2 h 30 min of wakefulness in dim light and 1 h 15 min of sleep in darkness (2:1 wake:sleep ratio), with the protocol ending after the last wake period. This schedule compressed the typical 24-hour day into an ultradian 3 h 45 min cycle to decouple circadian and homeostatic influences on physiology and behaviour. During each wake interval, participants completed repeated assessments of visual psychophysics (chromatic temporal contrast sensitivity), pupillometry with silent-substitution stimuli, ocular structure (optical coherence tomography) and physiology (intraocular pressure), psychomotor vigilance, salivary hormones, and standardised questionnaires, alongside continuous actigraphy, electrocardiography, and recordings of core and peripheral temperature, blood pressure, and interstitial glucose. Two supplementary evening sessions under experimental light exposure and dim-light conditions provide comparison data on circadian phase (salivary melatonin concentration, dim-light melatonin onset). Data collected from one pilot participant and screenings of two excluded candidates are additionally included. This dataset supports reuse for investigating circadian dynamics across multiple domains beyond the retinal-function hypotheses of the original study.

neuroscience↗

bioRxiv2026

Long noncoding RNA NRAV can regulate interferon-stimulated gene expression in melanoma

The long non-coding RNA Negative Regulator of Antiviral Response (NRAV) is known to suppress antiviral immunity by regulating interferon response, but its functional role in tumor immunology remains poorly understood. We examined the relevance of NRAV in melanoma and found that high NRAV expression was associated with poor survival, reduced inflammatory pathway activation, and resistance to immune checkpoint blockade. Bulk and single-cell transcriptomic profiling indicates that NRAV expression is selectively enriched in malignant cells suggesting a potential cancer cell-intrinsic function. To examine whether NRAV can regulate inflammatory responses in melanoma cells, we manipulated the levels of NRAV in the BRAF-mutant A375 melanoma model and characterized the expression of key interferon-stimulated genes (ISGs) following type-I and type-II interferon stimulation. Our findings reveal that the stable NRAV overexpression blunts the induction of key ISGs, whereas NRAV knockdown reciprocally amplifies their transcription. Subcellular fractionation revealed that NRAV is predominantly localized to the nuclear compartment of melanoma cells and the overexpression of NRAV altered regulatory histone marks on the target ISG promoters including MX1 and IFITM3. Collectively, these findings establish NRAV as a tumor-intrinsic epigenetic regulator of interferon signaling, highlighting its potential contribution to melanoma immune evasion.

cancer biology↗

bioRxiv2026

Age-driven Dysregulation of murine Dendritic Cells is controlled by cell-intrinsic and extrinsic effects

Aging is associated with chronic, low-grade inflammation and progressive immune dysfunction. However, the current understanding of age-associated changes in dendritic cells across tissues is scarce. Studies exploring ageing-associated changes in dendritic cells (DCs) have reported either a general decline in the overall DC compartment or subset-specific alterations affecting cDC1, cDC2, and pDC populations across spleen, lung and liver, underscoring the considerable inconsistencies across tissues and studies. To underpin whether age-associated changes are extrinsic or intrinsic we investigated DCs across bone marrow, six peripheral tissues and in in vitro bone marrow derived DC cultures to examine the effects of aging on DC-poiesis, tissue distribution, and cellular states related to DC functionality and activation. We discovered that aging selectively alters DC development in the bone marrow by reducing cDC progenitor populations while preserving pDC-poiesis. In peripheral tissues, however, age-associated changes in DC homeostasis were strongly tissue-dependent. The most significant shifts in cDC1 and cDC2 frequencies occurred in barrier tissues, such as the lung and small intestine. In contrast, the spleen and liver exhibited more limited or variable changes. These quantitative alterations were accompanied by tissue-specific changes in phenotypic and activation-associated markers, including CD24, CD103, CD11b, MHCII, and CD86. Single-cell transcriptomic analyses of senescent p21-expressing DC across tissues and subsets indicated localized inflammatory states that aligned with local macrophage populations, pointing toward cell-extrinsic niches that contribute to local age-associated dysfunction. Notably, aged bone marrow retained the capacity to efficiently generate DCs in in vitro Flt3L cultures, and antigen-presenting function of BMDC to CD4 and CD8 T cells was maintained, pointing towards preserved cell-intrinsic functions, albeit subset-specific differences in activation and inhibitory receptor expression in response to different pattern-recognition receptor agonists. Collectively, our findings indicate that aging does not superimpose a uniform alteration module to the DC compartment across tissues, but instead promotes selective alterations in DC ontogeny and tissue-specific remodeling of DC phenotypes and cellular states.

immunology↗

bioRxiv2026

Diverse high-fat diets drive multi-omic reprogramming that persists after dietary reversal

Dietary fat composition modulates host physiology and the gut microbiome, but the long-term effects of specific fat sources and the extent to which these changes resolve after dietary reversal remain incompletely defined. Here, we present a longitudinal multi-omic resource of mice maintained for one year on a purified control diet, seven high-fat diets differing in predominant fat source, or reversal regimens in which animals were switched from high-fat to control diet after 4 or 9 months. We further incorporated two cohorts with distinct pre-existing microbiome configurations to determine how baseline community structure shapes diet-induced remodeling of the gut microbiome ecosystem. By integrating longitudinal phenotyping, fecal metagenomics, fecal metabolomics, plasma metabolomics and lipidomics, and intestinal single-cell RNA sequencing, we defined the shared and dietary fat-specific responses across host and microbiome compartments. Baseline microbiome composition strongly influenced microbial responses to diet, indicating that pre-existing community structure is a major determinant of dietary ecosystem remodeling. Although many altered features shifted toward baseline after dietary reversal, only approximately half of diet-associated microbial changes recovered within the study window. A subset of taxa exhibited persistent alterations, including sustained depletion of Lactobacillus johnsonii and Bifidobacterium pseudolongum and sustained enrichment of Alistipes finegoldii, consistent with a "microbiome memory" of prior high-fat diet exposure. This memory effect is mirrored in the host, by sustained suppression of major histocompatibility complex class II (MHC-II) gene expression in intestinal epithelial cells after dietary reversal. These findings indicate that dietary fats leave a lasting imprint on the host-microbiome interactome that survives dietary intervention. Together, these data establish a resource for defining how dietary fat source, baseline microbiome composition, and dietary history shape host-microbiome states. The entire resource is available online as an RShiny app.

systems biology↗

bioRxiv2026

Divergent mitochondrial and metabolic adaptations shape selective vulnerability in ALS

Neurodegenerative diseases like amyotrophic lateral sclerosis (ALS) exhibit striking cell-type selectivity, yet the basis for this vulnerability remains elusive. Here, we uncover that even closely related neurons can harbor distinct mitochondrial properties that shape their response to disease. Using TOM-Tag, a circuit-based AAV-based strategy for cell type-specific mitochondrial immunopurification from projection neurons, we performed integrative proteomic, metabolomic, transcriptomic, and functional analyses of mitochondria from ALS-vulnerable corticospinal projection neurons (CSPNs) and resilient corticothalamic projection neurons (CTPNs) in vivo. We discovered that CSPNs and CTPNs exhibit divergent mitochondrial profiles at baseline, despite sharing cortical layer and developmental origin. CTPNs were primed for antioxidant buffering and fatty acid metabolism, whereas CSPNs were enriched for oxidative phosphorylation components. In ALS, CTPNs employed mitochondrial flexibility and redox defense, whereas CSPNs exhibited respiratory failure and metabolic stress. These findings reveal that intrinsic mitochondrial programs vary even between similar neurons, and that this hidden layer of diversity may critically shape susceptibility to neurodegeneration. By enabling high-resolution access to mitochondria in defined neuronal circuits, TOM-Tag offers a powerful new lens for dissecting disease mechanisms and identifying cell-specific therapeutic targets.

neuroscience↗

bioRxiv2025

Exercise intensity modulates the human plasma secretome and interorgan communication

Exercise is recognized as first-line therapy for many cardiometabolic diseases, including obesity, type 2 diabetes, and hypertension. Despite the abundant health-promoting effects of exercise, in-depth characterization of circulatory factors that mediate these benefits in humans remains incomplete. Moreover, how different modes and intensities of exercise uniquely regulate these processes is unclear. Here, we address these questions by conducting a multi-cohort human exercise intervention, incorporating sprint-interval exercise (SIE) and moderate-intensity exercise (MIE) to analyze intensity-dependent regulation of interorgan crosstalk. We find that exercise intensity distinctly influences the plasma proteome and metabolome in both untrained and trained participants. SIE led to immediate and robust changes to the plasma proteome, whereas MIE resulted in delayed secretory kinetics. By leveraging large, multi-organ gene and protein expression datasets, in combination with in vitro and in vivo tissue sampling, we map the differentially regulated proteins to their predicted tissue of origin and destination. We find that adipocytes are particularly sensitive to exercise intensity, undergoing broad transcriptomic remodeling following in vitro incubation with SIE as compared to MIE plasma. These findings underscore the integrated whole-body response following acute exercise and highlight exercise intensity as a key factor influencing interorgan communication.

physiology↗

bioRxiv2025

Tumor Genotype Dictates Mitochondrial and Immune Vulnerabilities in Liver Cancer

Although oncogenic alterations influence tumor metabolism, how they impose distinct metabolic programs within a shared tissue context remains poorly defined. Here, we developed a rapid mitochondrial profiling platform to compare metabolites and proteins in genetic models of primary liver cancer (PLC). Analyses of six genetically distinct PLCs revealed that mitochondrial energy metabolism is largely dictated by oncogene identity. Kras-driven tumors required creatine metabolism to buffer energy demands during early tumorigenesis, whereas c-MYC-driven tumors relied on oxidative phosphorylation. Among c-MYC-driven PLCs, Pten-deficient tumors accumulated mitochondrial phosphoethanolamine, a precursor for phosphatidylethanolamine (PE) synthesis. Inhibition of PE synthesis selectively impaired the growth of Pten-deficient tumors and extended survival, in part through enhanced infiltration of CD8 T cells and sensitization to TNF-mediated cytotoxicity. Mechanistically, loss of PE elevated surface TNF receptor 2 (TNFR2), promoting TNF signaling and pro-inflammatory response. These findings uncover genotype-specific mitochondrial metabolic liabilities and establish PE synthesis as a tumor-intrinsic mechanism of immune evasion in PLC.

cancer biology↗

bioRxiv2025

Intergenerational Conditioning via Intermittent Parental Hypoxia Confers Stroke Resilience in Offspring

Background and AimsIntergenerational disease transmission, where parental exposures or experiences influence disease susceptibility in offspring, may represent a crucial layer of stroke risk that extends beyond genetics alone. Environmental conditioning, such as intermittent sub-lethal hypoxia, can induce adaptive protective stress responses in the brain. However, whether such parental conditioning enhances offspring resilience to cerebral ischaemia remains unclear. This study investigates whether intermittent hypoxia in parents acts as an intergenerational conditioning stimulus, conferring resilience to ischaemic stroke in offspring, and explores associated molecular mechanisms. MethodsMale and female Balb/C mice (F0) were exposed to intermittent hypoxia (8% O2, 2 hours every other day, 16 cycles) prior to mating. To confirm that intermittent hypoxia induced neuroprotection in the parental generation, a separate cohort of F0 mice underwent transient middle cerebral artery occlusion (tMCAO). Offspring (F1) were generated from hypoxia-exposed F0 breeders and divided into four groups: biparental hypoxia, paternal hypoxia, maternal hypoxia, and normoxic controls. Adult F1 offspring also underwent tMCAO to model ischaemic stroke. Infarct volume and brain swelling were assessed 48 hours post-ischaemia. In a subgroup of F1 offspring, tandem mass tag (TMT)-based proteomic analysis of injured brain tissue was performed post-stroke to identify molecular pathways associated with neuroprotection. ResultsParental intermittent hypoxia significantly reduced infarct size and swelling in F0 mice. These protective effects were inherited by F1 offspring, with biparental exposure producing the greatest reduction in infarct volume, followed by maternal-only and paternal-only groups, and exhibiting sex-specific differences. Proteomic profiling revealed distinct treatment and lineage clusters. Key pathways implicated in offspring neuroprotection included metabolic regulation, immune signalling, cytoskeletal organisation, and cell survival, notably involving PI3K-Akt and EGFR pathways. ConclusionsIntermittent hypoxia in parents acts as an intergenerational conditioning stimulus, conferring offspring resilience to ischaemic stroke. This neuroprotective phenotype is supported by coordinated molecular adaptations in key pathways involved in survival and stress response. These findings highlight the potential for parental environmental conditioning to shape stroke outcomes in offspring, opening new avenues for therapeutic exploration.

neuroscience↗

bioRxiv2025

Novel biomarkers in mutation-specific gene profiles highlight the involvement of COL9A3 in cancer cell plasticity in uveal melanoma

UM is a deadly ocular malignancy with well-described genetic alterations that predict disease outcome. However, our current understanding of the biological underpinnings of high-risk uveal melanoma progression remains relatively limited. On the basis of RNA expression profiles, we identified 12 novel biomarkers associated with high-risk UM, with protein expression validation of the 2 top markers RBFOX2 and COL9A3. Moreover, we investigated the functional contribution of COL9A3 via its overexpression in low-risk and high-risk UM cell lines. Our data suggest that COL9A3 enhances cell motility and cell proliferation and alters morphology specifically in high-risk UM cells. Furthermore, zebrafish xenograft studies revealed improved cell dissemination in a low-risk UM cell line upon overexpression of COL9A3, whereas a high-risk UM cell line remained under wild-type conditions. Interestingly, RNA sequencing revealed a high-stress profile in high-risk UM cell lines overexpressing COL9A3 and suggested the upregulation of plasticity markers, such as CD44, Nestin, EZH2, ABCB5, PAX3 and CD166, as a coping mechanism. These markers are known as differentiation markers during the development of melanocyte biogenesis and are implicated in plasticity in other high-risk cancers. The relationship between COL9A3 and plasticity was validated by multiplex immunohistochemistry of FFPE tissue, which demonstrated colocalization of COL9A3, CD44 and Nestin. BAP1mut-UM samples presented higher levels of COL9A3, CD44 and Nestin expression than EIF1AXmut- or SF3B1mut UM samples did. A positive correlation between COL9A3 and Nestin expression in triple-positive cells, regardless of the UM subtype, was observed. Together, our data suggest that COL9A3 is a novel high-risk biomarker that may be involved in UM cell plasticity and is most prevalent in BAP1mut UM.

cancer biology↗

bioRxiv2025

Transcriptional regulators FOXD1 and RBFOX2 contribute to metastatic capacity in BAP1mut uveal melanoma

Uveal melanoma is the most prevalent primary intraocular cancer, with a significant metastatic risk. This risk is dependent on the genetic drivers. Secondary mutations in EIF1AX, SF3B1 and BAP1 correlate with clinical outcomes and are recognized for their distinct transcriptomic and epigenetic profiles. Previously, we identified 480 genes involved in the development of ocular melanocytes. Top ranking genes RBFOX2 and FOXD1 were significantly associated with BAP1 UM and were independently correlated to poor progression. However, it is uncertain whether either RBFOX2 or FOXD1 have biological contribution to disease progression or are solely indicative. This study investigates if and how these high-risk associated transcription regulators FOXD1 and RBFOX2 could influence tumor progression through knock-out and overexpression models. Our results indicate that loss of RBFOX2 affects cell morphology, attachment and proliferation, particularly in BAP1neg cells. Additionally, both RBFOX2 and FOXD1 contribute to tumor growth and dissemination in zebrafish xenografts. Loss of either RBFOX2 or FOXD1 reduced tumor volume and cell dissemination, with the greatest effects seen in BAP1neg cells. Overexpression models demonstrated different morphological and invasive behavior depending on the genetic background, suggesting complex roles in a context dependent fashion. Overexpression of RBFOX2 did not alter BAP1pos cells yet made BAP1neg cells more aggressive in vitro and in vivo. This study underscores the influence of RBFOX2 and FOXD1 as important factors for UM progression.

cancer biology↗

bioRxiv2024

CENcyclopedia: Dynamic Landscape of Kinetochore Architecture Throughout the Cell Cycle

The kinetochore, an intricate macromolecular protein complex located on chromosomes, plays a pivotal role in orchestrating chromosome segregation. It functions as a versatile platform for microtubule assembly, diligently monitors microtubule binding fidelity, and acts as a force coupler. Comprising over 100 distinct proteins, many of which exist in multiple copies, the kinetochores composition dynamically changes throughout the cell cycle, responding to specific timing and conditions. This dynamicity is important for establishing functional kinetochores, yet the regulatory mechanisms of these dynamics have largely remained elusive. In this study, we employed advanced quantitative immunofluorescence techniques to meticulously chart the dynamics of kinetochore protein levels across the cell cycle. These findings offer a comprehensive view of the dynamic landscape of kinetochore architecture, shedding light on the detailed mechanisms of microtubule interaction and the nuanced characteristics of kinetochore proteins. This study significantly advances our understanding of the molecular coordination underlying chromosome segregation.

cell biology↗

bioRxiv2024

Identification of Interaction Partners of Outer Inflammatory Protein A: Computational and Experimental Insights into How Helicobacter pylori Infects Host Cells

Adherence to the gastric epithelium is an essential feature of Helicobacter pylori for its colonization. Outer membrane proteins (OMPs) play a pivotal role in adherence potentiating the survival of the microbe in the gastric tissue. Among these proteins, Outer inflammatory protein A (OipA) is a critical protein that is known to help bacteria to colonize on the host gastric epithelial cell surface. Although the role of OipA in the H. pylori attachment and the association between OipA-positive H. pylori strains and clinical outcomes have been demonstrated, there is limited information on the structural mechanism of the OipA action in the adherence of H. pylori to the gastric epithelial cell surface. Our study utilizes experimental and computational methodologies to investigate the interaction partners of OipA on the gastric epithelial cell surface. Initially, we performed a proteomic analysis to decipher the OipA interactome in the human gastric epithelial cells using a pull-down assay of the recombinant OipA and the membrane proteins of the gastric epithelial cells. Proteomic analysis has revealed 704 unique proteins that interacted with OipA. We have further analyzed 16 partners of OipA using molecular modeling tools. Structural findings obtained from the prediction of the protein-protein complexes of OipA and candidate partners unraveled 3 human proteins whose OipA interactions could base an explanation about how H. pylori recruits OipA for adherence. Altogether, the findings presented here provide insights into novel mechanisms of H. pylori and host interactions through OipA, reflecting the potential of these mechanisms and interactions as therapeutic targets to combat H. pylori infection. Key pointsO_LIOuter membrane proteins (OMPs) are an emerging topic in bacterial infection. C_LIO_LIOipA is a candidate for an adherence-receptor network on the gastric epithelial cell surface with H. pylori. C_LIO_LIOipA interactome partners on gastric epithelial cell surfaces are valuable therapeutic targets for the H. pylori infection. C_LI

microbiology↗

bioRxiv2023

GeneMAP: A discovery platform for metabolic gene function

Organisms maintain metabolic homeostasis through the combined functions of small molecule transporters and enzymes. While many of the metabolic components have been well-established, a substantial number remains without identified physiological substrates. To bridge this gap, we have leveraged large-scale plasma metabolome genome-wide association studies (GWAS) to develop a multiomic Gene-Metabolite Associations Prediction (GeneMAP) discovery platform. GeneMAP can generate accurate predictions, even pinpointing genes that are distant from the variants implicated by GWAS. In particular, our work identified SLC25A48 as a genetic determinant of plasma choline levels. Mechanistically, SLC25A48 loss strongly impairs mitochondrial choline import and synthesis of its downstream metabolite, betaine. Rare variant testing and polygenic risk score analyses have elucidated choline-relevant phenomic consequences of SLC25A48 dysfunction. Altogether, our study proposes SLC25A48 as a mitochondrial choline transporter and provides a discovery platform for metabolic gene function.

genomics↗

bioRxiv2023

TCGEx: A visual interface for multifaceted analyses of The Cancer Genome Atlas gene expression data

The Cancer Genome Atlas (TCGA) initiative has been essential for revealing key mechanisms in human cancer leading to the development of novel therapeutics. Analysis of the cancer transcriptomics data in the TCGA and other public repositories require coding skills that are associated with a steep learning curve for most non-specialists. To enable a wider utilization of these data, we introduce The Cancer Genome Explorer (TCGEx), a web-based visual data analysis interface that can perform a number of sophisticated analyses ranging from survival modeling and gene set enrichment analysis to unsupervised clustering and linear regression-based machine learning. In addition to providing access to preprocessed data from TCGA and immune checkpoint inhibition studies on cBioportal and CRI-iAtlas, the TCGEx platform allows users to upload and investigate their own data. Using this tool, we investigated the molecular subsets of human melanoma and identified microRNAs associated with intratumoral interferon signaling. We validated these findings using independent data from clinical trials involving immune check-point inhibitors for melanoma and other cancers. Moreover, our analyses unveiled a subset of cytokines predictive of positive responses to diverse immune checkpoint inhibitors prior to treatment initiation. Built on the R/Shiny framework, TCGEx modules offer customizable features to tailor the analysis to different study contexts and help generate publication-ready plots. TCGEx is freely available at https://tcgex.iyte.edu.tr, and it provides an interactive solution to extract meaningful insights from cancer transcriptomics data and guide scientific inquiry.

bioinformatics↗

bioRxiv2022

Reduced Folate Carrier 1 is Present in Retinal Microvessels and Contributes to the Regulation of The Inner Blood Retinal Barrier in Health and Retinal Ischemia

BackgroundReduced folate carrier 1 (RFC1; SLC19a1) is the main responsible transporter for the B9 family of vitamins named folates, which are essential for normal tissue growth and development. While folate deficiency resulted in retinal vasculopathy, the expression and the role of RFC1 in blood-retinal barrier (BRB) are not well known. MethodsWe used whole mount retinas and trypsin digested microvessel samples of adult mice. To knockdown RFC1, we delivered RFC1-targeted short interfering RNA (RFC1-siRNA) intravitreally; while, to upregulate RFC1 we delivered lentiviral vector overexpressing RFC1. Retinal ischemia was induced 1-hour by applying FeCl3 to central retinal artery. We used RT-qPCR and Western blotting to determine RFC1. Endothelium (CD31), pericytes (PDGFR-beta, CD13, NG2), tight-junctions (Occludin, Claudin-5 and ZO-1), main basal membrane protein (Collagen-4), endogenous IgG and RFC1 were determined immunohistochemically. ResultsOur analyses on whole mount retinas and trypsin digested microvessel samples of adult mice revealed the presence of RFC1 in the inner BRB and colocalization with endothelial cells and pericytes. Knocking down RFC1 expression via siRNA delivery resulted in the disintegration of tight junction proteins and collagen-4 in twenty-four hours, which was accompanied by significant endogenous IgG extravasation. This indicated the impairment of BRB integrity after an abrupt RFC1 decrease. Furthermore, lentiviral vector-mediated RFC1 overexpression resulted in increased tight junction proteins and collagen-4, confirming the structural role of RFC1 in the inner BRB. Acute retinal ischemia decreased collagen-4 and occludin levels and led to an increase in RFC1. Besides, the pre-ischemic overexpression of RFC1 partially rescued collagen-4 and occludin levels which would be decreased after ischemia. ConclusionIn conclusion, our study clarifies the presence of RFC1 protein in the inner BRB, which has recently been defined as hypoxia-immune-related gene in other tissues and offers a novel perspective of retinal RFC1. Hence, other than being a folate carrier, RFC1 is an acute regulator of the inner BRB in healthy and ischemic retinas.

neuroscience↗

bioRxiv2019

Papillary renal cell carcinomas rewire glutathione metabolism and are deficient in anabolic glucose synthesis

Papillary renal cell carcinoma (pRCC) is a malignant kidney cancer with a prevalence of 7-20% of all renal tumors. Proteome and metabolome profiles of 19 pRCC and patient-matched healthy kidney controls were used to elucidate the regulation of metabolic pathways and the underlying molecular mechanisms. Glutathione (GSH), a main reactive oxygen species (ROS) scavenger, was highly increased and can be regarded as a new hallmark in this malignancy. Isotope tracing of pRCC derived cell lines revealed an increased de novo synthesis rate of GSH, based on glutamine consumption. Furthermore, rewiring of the main pathways involved in ATP and glucose synthesis was observed at the protein level. In contrast, transcripts encoding for the respiratory chain were not regulated, which prompts for non-genetic profiling. The molecular characteristics of pRCC are increased GSH synthesis to cope with ROS stress, deficient anabolic glucose synthesis, and compromised oxidative phosphorylation, which could potentially be exploited in innovative anti-cancer strategies.\n\nSIGNIFICANCE STATEMENTWe applied proteome- and metabolome profiling to elucidate molecular features in malign papillary renal cell carcinomas. By this characterization, a reprogramming of the main metabolic pathways, such as gluconeogenesis and fatty acid- and amino acid metabolism were identified. The proteins involved in the respiratory chain and the corresponding enzymatic activities were strongly reduced in pRCC, showing an anti-correlation compared with the transcriptome. Similar to renal oncocytomas, the ROS scavenger glutathione was identified as a hallmark in pRCC. Our results suggest that impaired metabolism and dysfunctional mitochondria determine the fate of pRCC. Furthermore, we propose that the specific regulation of the mitochondrial respiratory chain can differentiate highly similar malignant pRCCs from benign renal oncocytomas.

cancer biology↗

bioRxiv2019

Metabolic reprogramming and elevation of glutathione in chromophobe renal cell carcinomas

Chromophobe renal cell carcinomas (chRCC) are derived from intercalated cells of the collecting duct system, and are thought to be the malignant counterpart of benign renal oncocytomas. Here, we report the characterization of nine chRCC with adjacent healthy kidney tissues by applying proteome-, transcriptome (TCGA)-, and metabolome profiling. Most strikingly, the reactive oxygen species scavenger glutathione was significantly elevated in chRCC, caused by down-regulated enzymes involved in glutathione degradation. Metabolic reprogramming including stalled gluconeogenesis, down-regulated fatty acid- and amino acid metabolism was identified, even though, the abundance of amino acids and \"energy carrier\" molecules were unchanged. A striking anti-correlation of the mitochondrial respiratory chain between the transcriptome and the proteome was discovered, the transcripts coding for the respiratory chain were up-, while corresponding proteins and enzymatic activities were down-regulated. Similar to renal oncocytomas, chRCC exhibited a significant increase in glutathione, but are distinguishable by distinct regulation of the respiratory chain.

cancer biology↗